rs3118526

chr9-134445511-T-Cchr9-134445511-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061841.1(LOC105376311):n.309T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,148 control chromosomes in the GnomAD database, including 60,922 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (60922 hom., cov: 30)
• Consequence: LOC105376311 XR_007061841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62

Genes affected

LOC105376311 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376311	XR_007061841.1	n.309T>C		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135716 AN: 152030 Hom.: 60878 Cov.: 30

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.857

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.893 AC: 135816 AN: 152148 Hom.: 60922 Cov.: 30 AF XY: 0.891 AC XY: 66214 AN XY: 74352

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.853

Alfa AF: 0.867 Hom.: 76741

Bravo AF: 0.890

Asia WGS AF: 0.787 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.10

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3118526; hg19: chr9-137337357; COSMIC: COSV62683941;